Update NACHO modules from nf core #319
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| branches: | |
| - dev | |
| - master | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
| NFT_VER: "0.9.2" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: "${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }}" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanostring') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| test_profile: | |
| - "test" | |
| - "test_scores" | |
| - "test_samples" | |
| compute_profile: | |
| - "docker" | |
| - "singularity" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| compute_profile: "conda" | |
| - isMaster: false | |
| compute_profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.compute_profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.compute_profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Miniconda | |
| if: matrix.compute_profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.compute_profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install pdiff to see diff between nf-test snapshots | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pdiff | |
| - uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Run Tests (${{matrix.NXF_VER}} | ${{matrix.test_profile}} | ${{matrix.compute_profile}}) | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --tag ${{matrix.test_profile}} \ | |
| --profile "+${{ matrix.compute_profile }}" \ | |
| --junitxml=test.xml \ | |
| --debug --verbose | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml | |
| annotate_only: true |